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Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.

Ilyas M, Kim JS, Cooper J, Shin YA, Kim HM, Cho YS, Hwang S, Kim H, Moon J, Chung O, Jun J, Rastogi A, Song S, Ko J, Manica A, Rahman Z, Husnain T, Bhak J - BMC Genomics (2015)

Bottom Line: Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes.Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

View Article: PubMed Central - PubMed

Affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. milyaskh@hotmail.com.

ABSTRACT

Background: Pakistan covers a key geographic area in human history, being both part of the Indus River region that acted as one of the cradles of civilization and as a link between Western Eurasia and Eastern Asia. This region is inhabited by a number of distinct ethnic groups, the largest being the Punjabi, Pathan (Pakhtuns), Sindhi, and Baloch.

Results: We analyzed the first ethnic male Pathan genome by sequencing it to 29.7-fold coverage using the Illumina HiSeq2000 platform. A total of 3.8 million single nucleotide variations (SNVs) and 0.5 million small indels were identified by comparing with the human reference genome. Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes. SNVs were annotated for health consequences and high risk diseases, as well as possible influences on drug efficacy. We confirmed that the Pathan genome presented here is representative of this ethnic group by comparing it to a panel of Central Asians from the HGDP-CEPH panels typed for ~650 k SNPs. The mtDNA (H2) and Y haplogroup (L1) of this individual were also typical of his geographic region of origin. Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.

Conclusions: We present a whole-genome sequence and analyses of an ethnic Pathan from the north-west province of Pakistan. It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

Show MeSH
Admixture results of Pathan (PTN) individual to other ethnic groups in South Asia. Admixture results for K = 2 and K = 5 for the Pathan individual combined with eight ethnic genomes from HGDP dataset. The analysis was based on 643,281 SNVs. Each individual is represented by a vertical line, divided into colored segments that represent membership coefficients in the subgroups.
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Fig2: Admixture results of Pathan (PTN) individual to other ethnic groups in South Asia. Admixture results for K = 2 and K = 5 for the Pathan individual combined with eight ethnic genomes from HGDP dataset. The analysis was based on 643,281 SNVs. Each individual is represented by a vertical line, divided into colored segments that represent membership coefficients in the subgroups.

Mentions: We investigated how representative our Pathan genome was of that ethnic group by comparing it to another twenty-two Pathan individuals in the HGDP-CEPH panel [7], which had been typed for ~650 k SNVs, together with a further 190 individuals from another eight South Asian (Pakistani) populations from the same panel. Admixture analysis was performed based on 643,281 SNVs (thinned to avoid LD). We considered the cluster membership from STRUCTURE (from K = 2 to K = 5), the Pathan (PTN) genome composition was within the variability observed within the Pathan sample from the HGDP (Figure 2). Similarly, in a multi-dimensional scaling (MDS) plot, the Pathan genome fell within the other Pathan individuals (Additional file 1: Figure S4). Taken together, these two results confirm that the Pathan genome presented in this paper is representative of the Pathan ethnic group. These results are also in line with the self-reported ancestry of the subject, with all his grandparents coming from Afghanistan to Khyber Pakhtunkhwa (Pakistan).Figure 2


Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.

Ilyas M, Kim JS, Cooper J, Shin YA, Kim HM, Cho YS, Hwang S, Kim H, Moon J, Chung O, Jun J, Rastogi A, Song S, Ko J, Manica A, Rahman Z, Husnain T, Bhak J - BMC Genomics (2015)

Admixture results of Pathan (PTN) individual to other ethnic groups in South Asia. Admixture results for K = 2 and K = 5 for the Pathan individual combined with eight ethnic genomes from HGDP dataset. The analysis was based on 643,281 SNVs. Each individual is represented by a vertical line, divided into colored segments that represent membership coefficients in the subgroups.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4362645&req=5

Fig2: Admixture results of Pathan (PTN) individual to other ethnic groups in South Asia. Admixture results for K = 2 and K = 5 for the Pathan individual combined with eight ethnic genomes from HGDP dataset. The analysis was based on 643,281 SNVs. Each individual is represented by a vertical line, divided into colored segments that represent membership coefficients in the subgroups.
Mentions: We investigated how representative our Pathan genome was of that ethnic group by comparing it to another twenty-two Pathan individuals in the HGDP-CEPH panel [7], which had been typed for ~650 k SNVs, together with a further 190 individuals from another eight South Asian (Pakistani) populations from the same panel. Admixture analysis was performed based on 643,281 SNVs (thinned to avoid LD). We considered the cluster membership from STRUCTURE (from K = 2 to K = 5), the Pathan (PTN) genome composition was within the variability observed within the Pathan sample from the HGDP (Figure 2). Similarly, in a multi-dimensional scaling (MDS) plot, the Pathan genome fell within the other Pathan individuals (Additional file 1: Figure S4). Taken together, these two results confirm that the Pathan genome presented in this paper is representative of the Pathan ethnic group. These results are also in line with the self-reported ancestry of the subject, with all his grandparents coming from Afghanistan to Khyber Pakhtunkhwa (Pakistan).Figure 2

Bottom Line: Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes.Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

View Article: PubMed Central - PubMed

Affiliation: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. milyaskh@hotmail.com.

ABSTRACT

Background: Pakistan covers a key geographic area in human history, being both part of the Indus River region that acted as one of the cradles of civilization and as a link between Western Eurasia and Eastern Asia. This region is inhabited by a number of distinct ethnic groups, the largest being the Punjabi, Pathan (Pakhtuns), Sindhi, and Baloch.

Results: We analyzed the first ethnic male Pathan genome by sequencing it to 29.7-fold coverage using the Illumina HiSeq2000 platform. A total of 3.8 million single nucleotide variations (SNVs) and 0.5 million small indels were identified by comparing with the human reference genome. Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes. SNVs were annotated for health consequences and high risk diseases, as well as possible influences on drug efficacy. We confirmed that the Pathan genome presented here is representative of this ethnic group by comparing it to a panel of Central Asians from the HGDP-CEPH panels typed for ~650 k SNPs. The mtDNA (H2) and Y haplogroup (L1) of this individual were also typical of his geographic region of origin. Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.

Conclusions: We present a whole-genome sequence and analyses of an ethnic Pathan from the north-west province of Pakistan. It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

Show MeSH